Fresh Skin Biopsies Research Articles

Pathogenic variants in the SPTLC1 gene cause hyperkeratosis lenticularis perstans.

Hyperkeratosis lenticularis perstans (HLP), also known as Flegel disease, is a rare skin disease presenting with asymptomatic small hyperkeratotic papules. The lesions often appear on the dorsal feet and lower legs, and typically develop after the fourth decade of life. A genetic basis for HLP is suspected; however, so far no gene defect linked to the development of HLP has been identified. We aimed to identify the genetic cause of HLP. For mutational analysis we studied a cohort of five patients with HLP using next-generation sequencing (NGS). We used DNA -extracted from fresh skin biopsies alongside ethylenediamine tetraacetic acid (EDTA) blood samples from two patients, and formalin-fixed -paraffin-embedded skin biopsy material from three patients. In addition, immunofluorescence staining of HLP lesions from four patients was investigated. In all samples from the five patients with HLP we identified by NGS rare variants in the SPTLC1 gene. In four patients we detected small deletions/frameshift variants and in one patient a splicing variant, predicted to disturb the splicing process. In blood samples the detected variants were heterozygous with an allele frequency of 49% and 50%, respectively. In skin biopsies the allele frequency was within the range of 46-62%. Immunofluorescence staining revealed reduced SPTLC1 protein levels in skin of patients. Our findings suggest that pathogenic variants in the SPTLC1 gene are the underlying genetic cause of HLP. Of note, the identified variants were either frameshift- or splicing variants probably leading to nonsense-mediated mRNA decay and thus reduced SPTLC1 protein levels. We conclude that diminished SPTLC1, the key enzyme in sphingolipid biosynthesis, leads to the development of HLP, which highlights the sphingolipid pathway as a new therapeutic target.

Characterization and Expression Profiling of KRTAP9.2 at Different Developmental Stages of Pashmina Fiber in Changthangi Goat

Background: Keratin-associated protein’s (KRTAPs) are the major constituent proteins of cashmere fibre and have been implicated to have an important effect on the quality traits of this commercially valuable fibre. The objective of the present study was to determine the molecular characteristics of KRTAP9.2 gene in Pashmina (Cashmere) goat, known as Changthangi breed in J and K, India and well known for its finest fiber quality. Methods: We have studied the KRTAP9.2 gene expression status in hair follicles at different fiber development stages viz Anagen (growth) and Telogen (rest) in Changthangi goats of Kashmir and Ladakh region by performing quantitative Real Time PCR from fresh skin biopsies using gene specific primers. Furthermore, KRTAP9.2 structural models were generated and validated using various Bioinformatic tools. Result: Phylogenetic studies reveal close relation of KRTAP9.2 gene with Pantholops hodgsonii KRTAP9.2 (XM-005964828.1) and Ovis aries musimon KRTAP9.9 (XM-012152535.1). In our study we predicted a total of 20 KRTAP9.2 protein structures by QUARK and LOMET server and 5 structures by RaptorX, moreover, the validity of predicted structures was checked by using different parameters like RMSD value, C-Score, TM-value and ramachandran values, all parameters suggested structure predicted by RaptorX as better in our case. Real time PCR results showed expression of KRTAP9.2 in Pashmina hair follicles with a higher expression at the Telogen stage as compared to the Anagen stage. Owing to the structural importance of KRTAPs, such studies are indispensable for deciphering the molecular mechanism of pashmina growth which in turn will improve production, quality and diversity of pashmina fiber.

Labeling and tracking of immune cells in ex vivo human skin.

Human skin harbors various immune cells that are crucial for the control of injury and infection. However, the current understanding of immune cell function within viable human skin tissue is limited. We developed an ex vivo imaging approach in which fresh skin biopsies are mounted and then labeled with nanobodies or antibodies against cell surface markers on tissue-resident memory CD8+ T cells, other immune cells of interest, or extracellular tissue components. Subsequent longitudinal imaging allows one to describe the dynamic behavior of human skin-resident cells in situ. In addition, this strategy can be used to study immune cell function in murine skin. The ability to follow the spatiotemporal behavior of CD8+ T cells and other immune cells in skin, including their response to immune stimuli, provides a platform to investigate physiological immune cell behavior and immune cell behavior in skin diseases. The mounting, staining and imaging of skin samples requires ~1.5 d, and subsequent tracking analysis requires a minimum of 1 d. The optional production of fluorescently labeled nanobodies takes ~5 d.

Assessing the Feasibility and Limitations of Cultured Skin Fibroblasts for Germline Genetic Testing in Hematologic Disorders

Introduction Peripheral blood is the standard tissue source for germline genetic testing in most scenarios. In patients with hematologic malignancies, however, peripheral blood frequently contains tumor- or clonal hematopoiesis-related acquired genetic variants, often occurring in genes that can also cause inherited cancer susceptibility if present in the germline. Thus, an alternative tissue source is necessary. Cultured skin fibroblasts have been used as a potentially ideal alternative because they are free from blood contamination and provide ample DNA yields, advantages that other alternatives such as saliva or nail clippings lack. However, optimal culture methods, expected time from biopsy to sufficient DNA yield, culture failure rate, and limitations of this technique, including the possibility of variants being acquired solely due to the culturing process, are not yet known. Methods We conducted a retrospective cohort study of subjects with cytopenias or hematologic malignancies who underwent skin biopsy and fibroblast culture for germline genetic testing from April 2014 to June 2018. Skin biopsy culture technical data, including time from biopsy to culture set-up, shipment from an outside institution, culture failure, and biopsy size, were abstracted from tissue culture logs. Patient demographics, comorbidities, medication history, and hematologic diagnosis and treatment were abstracted from medical records. Next generation sequencing data from targeted capture of 144 inherited cancer and bone marrow failure predisposition genes obtained for clinical genetic testing purposes were analyzed to identify variants at both germline (40-60%) and subclonal (10-40%) variant allele frequencies (VAF). Pathogenicity was interpreted according to ACMG/AMP guidelines. Fisher's exact tests and logistic regression models were used to assess associations with culture failure. T-tests and linear regression models were used to assess factors associated with mean time to confluency. Results In total, we studied 350 samples from unique patients, including 61 (24%) who carried one or more pathogenic or likely pathogenic cancer susceptibility gene variant(s). Overall, 16 of the 350 (5%) biopsies failed to grow in culture. The median time from skin biopsy to sufficient growth to extract DNA for genetic testing was 27 days (IQR 22-29 days). Culture failure was significantly more likely in samples with a delay in culture initiation for 24 hours post biopsy (OR=4.32; p<0.01), and a pathogenic germline variant in a gene associated with telomere maintenance (OR=64.50; p<0.01). Factors associated with an increased mean time to sufficient growth included prior allogeneic stem cell transplant (32.1 days versus 27.2 days; p<0.01) and prior intravenous (IV) steroid exposure (29.9 days versus 26.4 days; p<0.01). Among samples cultured successfully, carriers of any pathogenic germline variant had a significantly decreased mean time to sufficient growth (25.4 days versus 28.6 days; p<0.01). A pathogenic or likely pathogenic subclonal variant was identified in 11 (4%) subjects at a median VAF of 20%. Among eight of these with additional tissue available, the presence of the variant was confirmed in four (50%). In individual cases, we found evidence of loss of a pathogenic variant in the hematopoietic malignancy. In one patient with a pathogenic variant with a 50% VAF in the original skin culture, the variant was not present in a skin culture from a second, fresh skin biopsy done due to discordant phenotype. Conclusions Culturing of skin fibroblasts for germline genetic testing in patients with hematologic disorders has a high success rate, especially when cultures are initiated within 24 hours of collection, and adds on average 27 days to genetic testing turnaround time. From patients with a hereditary syndrome, most skin biopsies will culture with the exception of individuals with a short telomere syndrome. For this subset, a direct skin biopsy without culture may be necessary. Subclonal variants at VAFs relevant to interpretation of a germline test were found in 4% of cases. Half were confirmed in an alternative tissue. Etiology of the subclonal variants, whether acquired during the culturing process or due to mosaicism or sequencing biases was not always clear. Careful assessment of the clinical phenotype in interpreting and applying germline genetic results to patient care will always be warranted. Disclosures Godley: UptoDate, Inc.: Honoraria; Invitae, Inc.: Membership on an entity's Board of Directors or advisory committees. Segal:BMS: Consultancy, Research Funding; AbbVie: Consultancy; Merck: Consultancy; Astra Zeneca: Consultancy. Churpek:UpToDate, Inc: Honoraria.

EBS generalized severe is an inflammatory disease

Epidermolysis bullosa (EB) is a group of genetic disorders in which the skin is abnormally fragile. In EB simplex, the skin cells tend to fall apart because their internal scaffolding of keratin fibres is defective, due to mutations in the genes encoding keratins type 5 or 14 (KRT5 and KRT14). But people with the generalised, severe type of EB simplex (EBS‐GS) are sometimes more ill than would be expected just from a mechanical problem with the skin; some even die in infancy, usually from infection. This group from France and Scotland explored the possibility that EBS‐GS patients also have a faulty immune system. They re‐examined skin specimens taken previously for diagnostic purposes from 17 patients with EBS‐GS and also tested fresh skin biopsies and blister fluid from a further 10 patients. They consistently found more inflammatory cells and higher levels of chemicals which promote inflammation (cytokines) than normal. The findings were the same regardless of whether the sample was from blistered or normal‐looking skin and whether the fault was in KRT5 or KRT14. Markers for the cytokine Th17 were particularly high, encouraging them to treat three EBS‐GS patients with the anti‐Th17 drug Apremilast as used in psoriasis. All three reported a dramatic reduction in blisters within the first month, which lasted throughout treatment for up to 10 months, with minimal side‐effects. One patient stopped the Apremilast after 7 months because of nausea and the blistering came back 2 days later. This appears to be a promising new approach to treating EBS‐GS.

Facial lupus vulgaris neglected for 50 years

Tuberculosis (TB) is still a problem in the developed and underdeveloped countries, and cutaneous TB is a small part of extrapulmonary forms. Lupus vulgaris (LV) is the most common form of cutaneous TB among Western populations. In Morocco, scrofuloderma is the most common form of cutaneous TB followed by LV. LV results both from inoculation and from the endogenous spread through hematogenous or lymphatic route from an underlying infectious focus. We report a case of facial LV with a long delay in diagnosis of 50 years. A 59-year-old man presented with a right cheek slow-growing lesion for 50 years. Skin biopsy showed tuberculoid granulomas without caseous necrosis, and the culture of cutaneous biopsy was negative. The polymerase chain reaction of Mycobacterium complex-specific DNA sequences on a fresh skin biopsy material was positive. The patient was given antituberculous treatment with which lesion improved. The delayed diagnosis of 50 years is atypical, especially that the lesion had a display character. Delayed diagnosis of cutaneous TB will cause a significant increase in morbidity. Early diagnosis and treatment is the key to reduce the morbidity.

CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays

In five separate families, we identified nine individuals affected by a previously unidentified syndrome characterized by growth retardation, spine malformation, facial dysmorphisms, and developmental delays. Using homozygosity mapping, array CGH, and exome sequencing, we uncovered bi-allelic loss-of-function CDK10 mutations segregating with this disease. CDK10 is a protein kinase that partners with cyclin M to phosphorylate substrates such as ETS2 and PKN2 in order to modulate cellular growth. To validate and model the pathogenicity of these CDK10 germline mutations, we generated conditional-knockout mice. Homozygous Cdk10-knockout mice died postnatally with severe growth retardation, skeletal defects, and kidney and lung abnormalities, symptoms that partly resemble the disease's effect in humans. Fibroblasts derived from affected individuals and Cdk10-knockout mouse embryonic fibroblasts (MEFs) proliferated normally; however, Cdk10-knockout MEFs developed longer cilia. Comparative transcriptomic analysis of mutant and wild-type mouse organs revealed lipid metabolic changes consistent with growth impairment and altered ciliogenesis in the absence of CDK10. Our results document the CDK10 loss-of-function phenotype and point to a function for CDK10 in transducing signals received at the primary cilia to sustain embryonic and postnatal development.

Reference genes for studies in infectious parasitic diseases in five types of human tissues

Gene expression analyses based on messenger RNA (mRNA) expression require accurate data normalization. When using endogenous reference genes, these should be carefully validated. Validated reference genes vary greatly depending on tissue, cell subsets and experimental context. This study was aimed to identify reference genes that have more stable mRNA levels among individuals in peripheral blood mononuclear cells (PBMC); fresh skin biopsies; lung and brain autopsies as well as, skin biopsies formalin-fixed paraffin-embedded (FFPE). Therefore, 6 endogenous reference genes were evaluated by quantitative real-time polymerase chain reaction: 18S rRNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), TATA box-binding protein (TBP), beta-2-microbolin (B2M), ubiquitin C (UBC) and mitochondrially encoded ATP synthase 6 (MT-ATP6). Furthermore, validation of their stabilities and performance as reference genes was determined by geNorm and NormFinder programs. The results show that the most stable genes for PBMC and fresh skin biopsies were TBP and UBC; in FFPE lung autopsies and skin biopsies were GAPDH and B2M; and in FFPE brain autopsies were GAPDH and UBC. In addition, 18S rRNA was the least stable of all genes analyzed. These data concluded that even genes constitutively expressed have transcript level variations in different tissues as well as storage and experimental conditions. These observations suggest that suitable reference genes should be selected for normalization of gene expression data analysis.

CD98, a novel marker of transient amplifying human keratinocytes

Identification of plasma membrane markers of basal keratinocytes is essential for sorting basal cells and, subsequently, adult epidermal stem cells. In this study, we isolated caveolin-1-enriched microdomains from human HaCaT keratinocytes and identified proteins representing potential cell surface markers of the epidermis by a proteomic approach. The purification of this caveolae domain allowed us to characterize 53 proteins of which 26% were transmembrane and 32% associated-membrane proteins. One of them, CD98, was found to be co-localized with beta1 integrin at the plasma membrane of the basal keratinocytes of healthy human epidermis. We then isolated CD98-positive keratinocytes from fresh skin biopsies. Using clonogenic assays, we demonstrate that CD98 may be considered as a marker of transient amplifying human keratinocytes.

Rapid radiation-induction of ATM protein levels in situ

Ataxia-telangiectasia (A-T) is characterised by hypersensitivity to ionising radiation (IR), immunodeficiency, neurodegeneration and predisposition to malignancy. Mutations in the A-T gene (ATM) often result in reduced levels of ATM protein and/or compromise ATM function. IR induced DNA damage is known to rapidly upregulate ATM kinase activity/phosphorylation events in the control of cell cycle progression and other processes. Variable expression of ATM levels in different tissues and its upregulation during cellular proliferation indicate that the level of ATM is also regulated by mechanisms other than gene mutation. Here, we report on the IR induction of ATM protein levels within a number of different cell types and tissues. Induction had begun within 5 min and peaked within 2 h of exposure to 2 Gy of IR, suggesting a rapid post-translational mechanism. Low basal levels of ATM protein were more responsive to IR induction compared to high ATM levels in the same cell type. Irradiation of fresh skin biopsies led to an average three-fold increase in ATM levels while immunohistochemical analyses indicated "low expressing" cells within the basal layer with ten-fold increases in ATM levels following IR. ATM "high expressing" lymphoblastoid cell lines (LCLs) which were initially resistant to the radiation-induction of ATM levels also became responsive to IR after ATM antisense expression was used to reduce the basal levels of the protein. These results demonstrate that ATM is present in variable amounts in different tissue/cell types and where basal levels are low ATM levels can be rapidly induced by IR to saturable levels specific for different cell types. ATM radiation-induction is a sensitive and rapid radioprotective response that complements the IR mediated activation of ATM.

Skin-explant model to evaluate effectiveness of depletion of hla-alloreactive t-cells

Depletion of host specific alloreactive T-cells from donor lymphocytes is an attractive tool for donor lymphocyte infusions after stem cell grafting. We intended to establish a preclinical method to evaluate effectiveness and safety of this approach. The skin explant model is a powerful method to predict the risk of GvHD in the HLA-identical setting, and we adapted this model to the HLA-haploidentical situation. Unmanipulated donor T-cells are compared with donor T-cells following depletion of host specific T-cells. Prior to depletion donor MNC are incubated in the presence of irradiated recipient MNC and after a period of 5 days activated T-cells, positive for CD25, CD69, CD71 and HLA-DR, are magnetically removed (VarioMacs, Miltenyi). A repeat MLC of unmanipulated donor cells. Fresh skin biopsies are divided into pieces of 1 - 2 mm diameter and incubated with 106 cultured T-cells in 20% autologous serum for 72 hours, fixed in formaldehyde and stained with haematoxylin-eosin. Skin alterations are graded according to Learner et al. In 3 separate experiments undepleted cells caused subepidermal cleft formation corresponding to a grade III to IV GvHD reaction. In contrast, depleted cells showed only grade I alterations, as similarly observed in medium control. Our preliminary data suggest that this approach could represent a useful tool to determine effectiveness of magnetic depletion of alloreactive T-cells and be valuable to assess the safety of these cells prior to infusion.

Identification of Mycobacterium avium complex in sarcoidosis.

Cell wall-defective bacteria which later reverted to acid-fast bacilli have been isolated from sarcoid tissue. These have not been conclusively shown to be mycobacteria. Specific PCR assays were applied to identify mycobacterial nucleic acids in these cultured isolates and in fresh specimens obtained from patients with sarcoidosis. Positive amplification and hybridization were observed with Mycobacterium avium complex- and/or Mycobacterium paratuberculosis-specific probes in five of the six cultured isolates and two fresh skin biopsy samples and one cerebrospinal fluid specimen. There was no amplification or hybridization with Mycobacterium tuberculosis or M. avium subsp. silvaticum probes, respectively. Patients' sera were also tested for antibody reactivities by immunoblotting with M. paratuberculosis recombinant clones expressing the 36,000-molecular-weight antigen (36K antigen) (p36) and the 65K heat shock protein (PTB65K). All seven sarcoidosis, four of six tuberculosis, and all six leprosy patient serum specimens showed strong reactivity with p36 antigen. In contrast, 13 of 38 controls showed only weak reactivity with p36 (P = 0.002 for controls versus sarcoidosis samples). Similarly, PTB65K reacted with high intensity with sera from 5 of 5 sarcoidosis, 5 of 6 tuberculosis, and 5 of 6 leprosy patients, compared with its low-intensity reaction with 5 of 22 controls (P = 0.001 for controls versus sarcoidosis samples). This study demonstrates the isolation and/or identification of M. paratuberculosis or a closely related M. avium complex strain from sarcoid skin lesions and cerebrospinal fluid. Furthermore, the reactivity of antibodies in sarcoid patient sera against p36 and PTB65K antigens was comparable to the reactivity of sera obtained from patients with known mycobacterial disease. Collectively, these data provide further support for the theory of the mycobacterial etiology of sarcoidosis.

The use of Michel's transport medium for immunofluorescence and immunoelectron microscopy in autoimmune bullous diseases.

We report the use of Michel's solution, already a well established transport medium, in the combined use of direct immunofluorescence (IMF) and pre-embedding immunoelectron microscopy in 3 subepidermal bullous diseases--bullous pemphigoid (BP), epidermolysis bullosa acquisita (EBA) and dermal binding linear IgA disease (LABD). Our studies demonstrated that electron microscopy of normal skin maintained in Michel's medium for up to 28 days showed remarkable preservation of all components of the basement membrane zone, including the ultrastructure of the basal keratinocytes, dermoepidermal junction and papillary dermis. However, epidermal cell cytolysis occurred after just 48 hours. Immunoelectron microscopy using a gold probe has enabled us to localise the immunoreactants in bullous pemphigoid, epidermolysis bullosa acquisita and dermal-binding linear IgA bullous dermatoses. Our findings are comparable to and as equally reliable as those on immunoelectron microscopy of fresh skin biopsies with no loss of antigen deposition, and demonstrate an effective new use of a well established transport medium.

'Salla Disease'

Severe mental retardation, coarse facial features, clumsiness, and speech failure were common findings in three brothers and one female third-cousin of a family from northern Finland. All the patients had vacuolated lymphocytes in peripheral blood smears, and electron microscopy of fresh skin biopsy specimens showed abundant cytoplasmic inclusions in various types of cells of the skin. Eight lysosomal hydrolases were assayed in peripheral blood lymphocytes and cultured skin fibroblasts, but no enzyme deficiency was detected. Urinary excretion of mucopolysaccharides, amino acids, glycoasparagines, and oligosaccharides was normal. Clinical findings, course of the disease, and the presence of cytoplasmic inclusions, indicating lysosomal storage phenomenon, suggest that the patients suffer from a genetic lysosomal storage disorder not described earlier. The eponym "Salla disease" was introduced, referring to the geographically restricted area where the family resides.